phytools: fastMRCA – R documentation

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fastMRCA

Get the MRCA (or height above the root of the MRCA) of a pair of tip taxa

Description

This function returns the most recent common ancestor (node number) for a pair of taxa; or, in the case of fastHeight, the height above the root of the MRCA of a pair of taxa; or, in the case of fastDist, the patristic distance between a pair of taxa.

Usage

fastMRCA(tree, sp1, sp2)
fastHeight(tree, sp1, sp2)
fastDist(tree, sp1, sp2)

Arguments

`tree`	an object of class `"phylo"`.
`sp1`	species one name.
`sp2`	species two name.

Details

This function is mostly redundant with findMRCA (or findMRCA(...,type="height") in the case of fastHeight) but for very large trees will be considerably faster. (Also see getMRCA in the ape package.)

Value

The node number of the MRCA, the height above the root (for fastHeight), or the patristic distance between two taxa (for fastDist).

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

Examples

tree<-pbtree(n=2000)
anc<-fastMRCA(tree,"t1","t15")

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19